title: Prostate - PRC9 - 5726

status: Public on Aug 01 2009

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: Genome-wide expression levels with Affymetrix GeneChip Human Exon 1.0 ST arrays using RNA prepared from a fresh prostate cancer specimen.

hyb_protocol: Array hybridisation was performed according to the manufacturer's instructions (Affymetrix). Arrays were hybridised by rotating them at 60 rpm in the Affymetrix Gene Chip hybridisation oven at 45°c for 16 hours. After hybridisation, the arrays are washed in the Affymetrix GeneChip Fluidics station FS 450.

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix). The  arrays are scanned using the Affymetrix Gene Chip scanner 3000 7G system.

data_processing: Gene-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays using the multi-array analysis (RMA) algorithm implemented from the Affymetrix Power Tools (APT) software. Gene-level estimates were obtained using the ‘core’ metaprobe list annotation release 21.

source_name: Prostate 5726

label_protocol: The Affymetrix GeneChip Whole Transcript (WT) Sense Target Labelling Assay was used to generate amplified and biotinylated sense-strand DNA targets from the entire expressed genome (1.5 μ g of total RNA) without bias.

extract_protocol: Areas containing cancer and normal glands were then macrodissected from the OCT block using a fresh sterile scalpel blade and were used for RNA extraction. RNA was extracted from the tissue in TRIzol (Invitrogen Ltd, UK) by following the manufacturers instructions and purified using the RNeasy MinElute clean up kit (Qiagen Ltd, UK) according to the manufacturer’s instructions.

treatment_protocol: A small piece of tissue (approx 2 mm3) containing areas of cancer and/or normal glands was identified within the frozen prostate slice with the help of H&E stained whole mount sections from the adjacent formalin fixed slices. This piece of tissue was washed in ice cold PBS for 2 minutes, embedded in OCT embedding medium (Raymond Lamb UK, Ltd) and frozen on dry ice. Frozen sections obtained from this tissue were stained with H&E and high molecular weight cytokeratin to confirm the presence and location of cancer and normal glands within it.

value: Prostate

tag: Cancer Status

value: Cancer


title: N1 at 0h, biological replicate 1

status: Public on Aug 06 2009

type: RNA

city: Munich

first: Lothar

middle: J.

last: Strobl

address: Marchioninistr. 25

department: Department of Gene Vectors

country: Germany

institute: Helmholtz Zentrum München, German Research Center for Environmental Health

description: gene expression data from cells without induced Notch1-IC expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU 133 PLUS 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Notch1-IC expression 0h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

growth_protocol: Cells were estrogen depleted for 3 days and Notch1-IC, Notch2-IC, CAT and EBNA2 were induced for different time periods (0h, 4h, 8h, 24h). For expression of the transgene for 3 days, cells were estrogen depleted and the transgene was directly induced for viability purpose.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were pelleted and suspended in Trizol for further RNA isolation.

tag: EREB2-5 cells


title: N1 at 3d, biological replicate 2

description: gene expression data from cells under steady Notch1-IC expression for 3 days

source_name: Notch1-IC expression 3d


title: N1 at 8h, biological replicate 2

description: gene expression data from cells with 8h Notch1-IC expression

source_name: Notch1-IC expression 8h


title: Prostate - PRC6 - 6838

source_name: Prostate 6838

tag: Gender

value: Male

tag: Tissue


title: Prostate - PRC8 - 6838

description: Technical replicate of PRC6_2


title: Prostate - PRC5 - 2243

source_name: Prostate 2243


title: Prostate - PRC4 - 1586

source_name: Prostate 1586


title: Prostate - PRC3 - 1266

source_name: Prostate 1266


title: Prostate - PRC7 - 9454

source_name: Prostate 9454


title: embryoid body, microspheres, control, 10 days, replicate #3

status: Public on Aug 04 2009

city: Atlanta

first: Nathan

last: Bowen

state: GA

address: 223 James P Brawley Drive

department: Center for Cancer Research and Therapeutic Development

country: USA

institute: Clark Atlanta University

description: CEL and CHP files were generated by the Affymetrix Gene Chip Operating System (GCOS) default settings.

hyb_protocol: and hybridized to the Mouse Genome 430 2.0 Array according to manufacturer’s protocols (Affymetrix Inc.)

scan_protocol: scanned according to manufacturer’s protocols (Affymetrix Inc.)

organism: Mus musculus

label_protocol: Labeled cRNA from three micrograms of total RNA was generated using the One-Cycle Target Labeling and Control Reagents Kit (Affymetrix Inc.)

extract_protocol: Total RNA was extracted from undifferentiated ESCs and EBs using an RNeasy Mini kit (Qiagen Incorporated).

tag: ESCs (D3 line) were maintained in an undifferentiated state on gelatin-coated tissue culture plates in LIF-containing media as described previously.  EBs were formed from 2x106 ESCs inoculated in LIF-free media and cultured under rotary conditions.  EBs containing microspheres were produced by coating CellTracker Red or RA-loaded microspheres in 0.1% gelatin solution for 3 hours prior to mixing with ESCs in various microsphere to cell ratios and a range of rotary speeds.  EB media was exchanged every 1-2 days as needed.


title: Desulfovibrio Acetone Stress Slide 8

status: Public on Aug 08 2009

city: Knoxville

first: Qiang

last: He

state: TN

address: 57A Perkins Hall

department: Civil and Environmental Engineering

institute: The University of Tennessee

description: The objective of this study is to investigate the stress response of the sulfate-reducing bacterium Desulfovibrio vulgaris to elevated concentrations of acetone as a solvent, which is a common co-contaminant in subsurface environments.

data_processing: Lowess intensity-based normalization. He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Desulfovibrio vulgaris subjected to acetone stress

treatment_protocol: Culture was treated by 5% (v/v) acetone for 100 minutes

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase in standard Lactate-Sulfate medium followed by exposure to acetone as a stressor.

source_name: Desulfovibrio vulgaris control culture

treatment_protocol: Control culture without treatment

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase in standard Lactate-Sulfate medium without exposure to acetone as a stressor.


title: embryoid body, microspheres containing Retinoic Acid, 10 days, replicate #2

data_processing: CEL and CHP files were generated by the Affymetrix Gene Chip Operating System (GCOS) default settings.


title: embryoid body, microspheres, control, 10 days, replicate #1


title: embryoid body, microspheres, control, 10 days, replicate #2


title: embryoid body, microspheres containing Retinoic Acid, 10 days, replicate #1


title: Prostate - PRC24 - 2211

source_name: Prostate 2211


title: Prostate - PRC25 - 2007

source_name: Prostate 2007


title: Prostate - PRC31 - 4551

source_name: Prostate 4551


title: Prostate - PRC26 - 6923

source_name: Prostate 6923


title: Prostate - PRC21 - 10643

source_name: Prostate 10643


title: Prostate - PRC32 - 6469

source_name: Prostate 6469


title: Prostate - PRC22 - 10376

source_name: Prostate 10376


title: Prostate - PRC16 - Normal 3

description: Genome-wide expression levels with Affymetrix GeneChip Human Exon 1.0 ST arrays using RNA prepared from a fresh prostate normal specimen.

source_name: Prostate Normal 3

value: Normal


title: Prostate - PRC1 - 877

source_name: Prostate 877


title: Prostate - PRC2 - 908

source_name: Prostate 908


title: Prostate - PRC23 - 9134

source_name: Prostate 9134


title: Prostate - PRC20 - 10643


title: Prostate - PRC17 - 7962

source_name: Prostate 7962


title: Prostate - PRC15 - Normal 2

source_name: Prostate Normal 2


title: Prostate - PRC19 - 1073

source_name: Prostate 1073


title: Prostate - PRC14 - Normal 1

source_name: Prostate Normal 1


title: Prostate - PRC13 - 9742

source_name: Prostate 9742


title: Prostate - PRC18 - 9742


title: Prostate - PRC12 - 8935

source_name: Prostate 8935


title: Prostate - PRC40 - 877


title: Prostate - PRC10 - 2207

source_name: Prostate 2207


title: Prostate - PRC38 - 3128

source_name: Prostate 3128


title: Prostate - PRC35 - 1624

source_name: Prostate 1624


title: Prostate - PRC42 - 9454

source_name: Prostate 9454


title: Prostate - PRC11 - 8341

source_name: Prostate 8341


title: Prostate - PRC36 - 2211

source_name: Prostate 2211


title: Prostate - PRC30 - 8341


title: Prostate - PRC34 - 1624


title: Prostate - PRC29 - 543

source_name: Prostate 543


title: Prostate - PRC28 - 7960

source_name: Prostate 7960


title: Prostate - PRC39 - 6490

source_name: Prostate 6490


title: Prostate - PRC27 - 7355

source_name: Prostate 7355


title: N2 at 0h, biological replicate 1

description: gene expression data from cells without induced Notch2-IC expression

source_name: Notch2-IC expression 0h


title: ARCD kidney, HD123 [HG-U133B]

city: Rotterdam

first: Dmitry

last: Zubakov

state: ZH

address: Dr. Molewaterplein, 50

department: FMB

country: Netherlands

institute: Erasmus Medical Centre Rotterdam

description: Gene expression data for tumor kidney

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: The data were analyzed using R Bioconductor software and mas5 algorithm for data normalization and processing

source_name: tumor renal tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: tumor kidney


title: ARCD kidney, HD195 [HG-U133B]

description: Gene expression data for tumor kidney


title: ARCD kidney HD105 [HG-U133B]

description: Gene expression data for tumor kidney


title: Normal kidney, 13 weeks old fetus [HG-U133B]

description: Gene expression data for normal kidney

source_name: 13 weeks old normal renal tissue

tag: fetal normal kidney


title: ESRD kidney, HD94 [HG-U133B]

description: Gene expression data for tumor kidney


title: Chromophobe RCC, pooled# [HG-U133B]

description: Gene expression data for tumor kidney


title: Renal oncocytoma, pooled [HG-U133B]

description: Gene expression data for tumor kidney


title: ARCD kidney, HD209 [HG-U133B]

description: Gene expression data for tumor kidney


title: Conventional RCC, pooled, pT1, G1 [HG-U133B]

description: Gene expression data for tumor kidney


title: Normal adult kidney, pooled [HG-U133B]

description: Gene expression data for normal kidney

source_name: adult normal renal tissue

tag: adult normal kidney


title: ESRD kidney, HD217 [HG-U133B]

description: Gene expression data for tumor kidney


title: Conventional RCC, pooled, pT3, G3 [HG-U133B]

description: Gene expression data for tumor kidney


title: Clear cell sarcoma of the kidney [HG-U133B]

description: Gene expression data for tumor kidney


title: Pappilary renal cell tumor, pT3,G3 [HG-U133B]

description: Gene expression data for tumor kidney


title: Normal kidney, 12 weeks old fetus [HG-U133B]

description: Gene expression data for normal kidney

source_name: 12 weeks old normal renal tissue


title: Wilm's tumor [HG-U133B]

description: Gene expression data for tumor kidney


title: Pappilary renal cell tumor, pT1,G1 [HG-U133B]

description: Gene expression data for tumor kidney


title: Normal kidney, adult [HG-U133B]

description: Gene expression data for normal kidney

tag: adult normal kidney, pooled


title: Normal kidney, 21 weeks old fetus [HG-U133B]

description: Gene expression data for normal kidney

source_name: 21 weeks old normal renal tissue


title: Normal kidney, 20 weeks old fetus [HG-U133B]

description: Gene expression data for normal kidney

source_name: 20 weeks old normal renal tissue


title: P0.5 Atrx-null #3

city: London

first: Nathalie

last: Berube

state: Ontario

address: 800 Commissioners Road East

country: Canada

institute: Children's Health Research Institute

description: P0.5 Atrx-null #3

hyb_protocol: 10 μg of labeled cRNA was hybridized to Mouse Genome 2.0 GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 450. GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: Probe signal intensities for were generated using GCOS1.4 (Affymetrix Inc., Santa Clara, CA) using default values for the Statistical Expression algorithm parameters and a Target Signal of 150 for all probe sets and a Normalization Value of 1.

label: Biotin

source_name: forebrain, P0.5 Atrx-null #3

label_protocol: Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP.

extract_protocol: QIAGEN RNeasy Mini kit, manufacturer's protocol

tag: Strain

tag: Sex

value: male

tag: Age


title: P0.5 Atrx-null #2B

description: P0.5 Atrx-null #2B

source_name: forebrain, P0.5 Atrx-null #2B


title: ARCD kidney, HD209 [HG-U133A]

description: Gene expression data for tumor kidney


title: P0.5 Atrx-null #2A

description: P0.5 Atrx-null #2A

source_name: forebrain, P0.5 Atrx-null #2A


title: ESRD kidney, HD217 [HG-U133A]

description: Gene expression data for tumor kidney


title: P0.5 Atrx-null #1

description: P0.5 Atrx-null #1

source_name: forebrain, P0.5 Atrx-null #1


title: P0.5 wild type #1

description: P0.5 wild type #1

source_name: forebrain, P0.5 wild type #1


title: P0.5 wild type #3

description: P0.5 wild type #3

source_name: forebrain, P0.5 wild type #3


title: Conventional RCC, pooled, pT1, G1 [HG-U133A]

description: Gene expression data for tumor kidney


title: ESRD kidney, HD94 [HG-U133A]

description: Gene expression data for tumor kidney


title: Normal adult kidney, pooled [HG-U133A]

description: Gene expression data for normal kidney


title: Normal kidney, 20 weeks old fetus [HG-U133A]

description: Gene expression data for normal kidney


title: ARCD kidney HD105 [HG-U133A]

description: Gene expression data for tumor kidney


title: ARCD kidney, HD123 [HG-U133A]

description: Gene expression data for tumor kidney


title: E13.5 Atrx-null #2

description: E13.5 Atrx-null #2

source_name: forebrain, E13.5 Atrx-null #2


title: Chromophobe RCC, pooled# [HG-U133A]

description: Gene expression data for tumor kidney


title: P0.5 wild type #2

description: P0.5 wild type #2

source_name: forebrain, P0.5 wild type #2


title: Conventional RCC, pooled, pT3, G3 [HG-U133A]

description: Gene expression data for tumor kidney


title: E13.5 Atrx-null #3

description: E13.5 Atrx-null #3

source_name: forebrain, E13.5 Atrx-null #3


title: Renal oncocytoma, pooled [HG-U133A]

description: Gene expression data for tumor kidney


title: E13.5 wild type #3

description: E13.5 wild type #3

source_name: forebrain, E13.5 wild type #3


title: E13.5 wild type #1

description: forebrain, E13.5, wild type #1

scan_protocol: GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 450.  GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

source_name: forebrain, E13.5 wild type #1


title: E13.5 Atrx-null #1

description: E13.5 Atrx-null #1

source_name: forebrain, E13.5 Atrx-null #1


title: Pappilary renal cell tumor, pT1,G1 [HG-U133A]

description: Gene expression data for tumor kidney

source_name: tumor renal tissue


title: Pappilary renal cell tumor, pT3,G3 [HG-U133A]

description: Gene expression data for tumor kidney


title: ARCD kidney, HD195 [HG-U133A]

description: Gene expression data for tumor kidney


title: Wilm's tumor [HG-U133A]

description: Gene expression data for tumor kidney


title: E13.5 wild type #2

description: E13.5 wild type #2

source_name: forebrain, E13.5 wild type #2


title: Clear cell sarcoma of the kidney [HG-U133A]

description: Gene expression data for tumor kidney


title: WT 45oC 30min rep2

status: Public on Jul 31 2009

city: Toyonaka

first: Miyazaki

last: Toshiko

state: Osaka

address: 1-1 Machikaneyama

department: science

country: Japan

institute: Osaka univ.

description: gene expression data from log phase

hyb_protocol: 3'-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401a520105F GeneChip (Affymetrix, Santa Clara, CA). The array was incubated for 16 h at 50｡C in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 20 micro g of herring sperm DNA (Promega), 0.1 mg of bovine serum albumin (BSA), the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix), and then the array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The image data was scaled to the target intensity by one-step Tukeyﾕs biweight algorithm using GeneChip Operating Software, version 1.1 (Affymetrix, Santa Clara, CA).

organism: Thermus thermophilus HB8

source_name: wild-type T. thermophilus HB8 strains were each pre-cultured at 70oC and then at 45 C for 30 minutes

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 1.2 units of DNase I (GE Healthcare Bio-Science Corp.) at 37｡C for 10 min, and after inactivation at 98｡C for 10 min, the cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer課ｪs instructions (Affymetrix).

growth_protocol: wild-type T. thermophilus HB8 strains were each pre-cultured at 70oC for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (0.3 ml) were inoculated into 0.15 liter of the same medium and then cultivated at 70oC. At the Abs600=0.8 (0min), cold medium was added and the temperature were shifted down to 45oC. Cells were collected at 0min and 30min after  temperature shift, and then crude RNA was extracted.

extract_protocol: Cells were collected from 100 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol. This mixture was incubated at 65｡C for 5 min, chilled on ice for 5 min, and then centrifuged at 4｡C. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 0.2 ml of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37｡C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70｡C for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.


title: WT 0min rep2

description: gene expression data from log phase

source_name: wild-type T. thermophilus HB8 strains were each pre-cultured at 70oC


title: WT 0min rep3

description: gene expression data from log phase


title: WT 45oC 30min rep3

description: gene expression data from log phase


title: Deletion of ttcsp1 0 min rep3

description: gene expression data from log phase

source_name: ttcsp1 mutant T. thermophilus HB8 strains pre-cultured at 70 C

growth_protocol: ttcsp1 mutant T. thermophilus HB8 strains were each pre-cultured at 70oC for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (0.3 ml) were inoculated into 0.15 liter of the same medium and then cultivated at 70oC. At the Abs600=0.8 (0min), cold medium was added and the temperature were shifted down to 45oC. Cells were collected at 0min and 30min after  temperature shift, and then crude RNA was extracted.


title: Normal kidney, 21 weeks old fetus [HG-U133A]

description: Gene expression data for normal kidney

source_name: 21 weeks old normal renal tissue


title: WT 45oC 30min rep1

description: gene expression data from log phase


title: Deletion of ttcsp1 45oC 30min rep1

description: gene expression data from log phase

source_name: ttcsp1 mutant T. thermophilus HB8 strains pre-cultured at 70 C and then at 45 C for 30 minutes


title: Deletion of ttcsp1 45oC 30min rep2

description: gene expression data from log phase


title: Deletion of ttcsp1 45oC 30min rep3

description: gene expression data from log phase


title: Normal kidney, adult [HG-U133A]

description: Gene expression data for normal kidney

source_name: adult normal renal tissue


title: Deletion of ttcsp1 0 min rep2

description: gene expression data from log phase


title: WT 0min rep1

description: gene expression data from log phase


title: Deletion of ttcsp1 0 min rep1

description: gene expression data from log phase


title: Helicobacter hepaticus_wt versus fliA exp. 2 rep. 2

status: Public on Jul 14 2009

city: Hannover

first: Christine

last: Josenhans

address: Carl-Neuberg-Strasse 1

department: Institute for Medical Microbiology

institute: Hannover Medical School

description: Comparison of wild type to fliA mutant bacteria

hyb_protocol: according to manufacturer's recommendations

scan_protocol: scanned with Affymetrix 428 scanner

data_processing: data processing was done with IMAGENE and MAVI (MWG Biotech)

organism: Helicobacter hepaticus

source_name: Helicobacter hepaticus wild type bacteria

label_protocol: custom

extract_protocol: Qiagen RNAeasy

tag: grown in liquid culture

source_name: Helicobacter hepaticus fliA mutant


title: Helicobacter hepaticus_wt versus fliA exp. 3 rep. 2

source_name: Helicobacter hepaticus wt bacteria


title: Helicobacter hepaticus_wt versus fliA exp. 2 rep. 1


title: Helicobacter hepaticus_wt versus fliA exp. 3 rep. 1


title: SAP1ko Biological Replicate 1 (Cy5) vs. sgSpz Biological Replicate 1 (Cy3)

city: Seattle

first: Stefan

middle: H. I.

last: Kappe

state: WA

address: 307 Westlake Ave N, Suite 500

institute: Seattle Biomedical Research Institute

description: ooSpz: Sporozoites from P. yoelii (17XLN) infected A. stephensi mosquitoes were isolated from midguts at day 10 after infectious blood meal. sgSpz: Sporozoites from P. yoelii (17XLN) infected A. stephensi mosquitoes were isolated from salivary glands at day 15 after infectious blood meal. SAP1ko: Sporozoites from P. yoelii (17XLN) (SAP1 knock out) infected A. stephensi mosquitoes were isolated from salivary glands at day 15 after infectious blood meal.

hyb_protocol: For microarray hybridizations, 10 ug of aRNA was fragmented with the RNA fragmentation kit (Ambion), then coupled with Cy3 or Cy5 (Amersham) according to manufacturer's protocol (Amino Allyl Message Amp II aRNA Amplification Kit, Ambion). Each hybridization mixture (60 ml) contained 1-5 mg of the cy3 and cy5 labeled aRNA, 4 ug yeast tRNA (Invitrogen), 8 ug polyA RNA (Invitrogen), 10mg mouse Cot1 DNA (GE Healthcare), 0.2% SDS, 20mM Hepes pH 7.2 in 3xSSC. Samples were applied beneath lifterslips (Erie) onto microarray slides.  Hybridization of the labeled aRNA was done for 16 hrs in a 60C waterbath using hybridization chambers (Corning). Microarrays were removed from the hybridization chambers and washed in 1X SSC with 0. 1% SDS for 2 min at room temperature , 0.2X SSC for 2min, 0.05X SSC for 1min twice and 0.01X SSC for 30 sec. Slides were dried by centrifugation for 5 min at 60g.

scan_protocol: Scanned on an GenePix 4000A laser scanner. Images were quantified using GenePix Pro software (Axon Instruments Inc.).

data_processing: We processed and analyzed the expression data using the limma package for the R programming environment (Smyth GK, 2005), as follows. Background correction was performed using limma's "normexp" method, which ensures that there were no missing or negative corrected intensities. An offset of 50 was used for both channels to damp down the variability of the log-ratios for low-intensity spots. The resulting log-ratios were normalized by using print-tip loess method (Smyth GK and Speed T, 2003).

organism: Plasmodium yoelii

source_name: Total RNA from SAP1ko Biological Replicate 1 (Cy5) labeled with Cyanine-5 (red).

label_protocol: Total RNA from each sample were extracted using Trizol (Invitrogen) and DNase treated using Turbo-DNAfree (Ambion).Total RNA was then subjected to two rounds of linear amplification using the Amino Allyl Message Amp II aRNA Amplification Kit (Ambion) according to manufaturer's directions. The quality of total and amplified RNAs were examined with the Agilent 2100 BioanalyzerTM (Agilent Technologies, Palo Alto, CA) while the quantity of the RNA samples was assessed using a Nanodrop ND-1000 spectrophotometer prior to microarray hybridization.

extract_protocol: TriZol procedure

tag: P. yoelii SAP1 knock out, BALB/c mice, salivary glands

source_name: Total RNA from sgSpz Biological Replicate 1 (Cy3) labeled with Cyanine-3 (green).

tag: P. yoelii, A. stephensi mosquitoes, salivary glands


title: Helicobacter hepaticus_wt versus fliA exp. 1 rep. 2


title: Normal kidney, 13 weeks old fetus [HG-U133A]

description: Gene expression data for normal kidney

source_name: 13 weeks old normal renal tissue


title: sgSpz Biological Replicate 1 (Cy5) vs. SAP1ko Biological Replicate 1 (Cy3)

source_name: Total RNA from sgSpz Biological Replicate 1 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from SAP1ko Biological Replicate 1 (Cy3) labeled with Cyanine-3 (green).


title: sgSpz Biological Replicate 2 (Cy5) vs. SAP1ko Biological Replicate 2 (Cy3)

source_name: Total RNA from sgSpz Biological Replicate 2 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from SAP1ko Biological Replicate 2 (Cy3) labeled with Cyanine-3 (green).


title: Helicobacter hepaticus_wt versus fliA exp. 1 rep. 1

source_name: Helicobacter hepaticus fliA mutant bacteria


title: SAP1ko Biological Replicate 2 (Cy5) vs. sgSpz Biological Replicate 2 (Cy3)

source_name: Total RNA from SAP1ko Biological Replicate 2 (Cy5) labeled with Cyanine-5 (red).

source_name: Total RNA from sgSpz Biological Replicate 2 (Cy3) labeled with Cyanine-3 (green).


title: [gar-] sample #2

status: Public on Jul 01 2009

city: Cambridge

first: Jessica

middle: C. S.

last: Brown

state: MA

address: 9 Cambridge Center

department: biology

institute: Whitehead/MIT

description: [gar-] W303 yeast grown in 2% glucose medium to late exponential phase.

hyb_protocol: 15 micrograms cRNA was hybridized to Affymetrix S98 arrays following the manufacturer's protocols.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner.

data_processing: Data were condensed with MAS5 using default settings then processed using GCOS using deafult settings.  The scale factor was set to 500.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: planktonic yeast, late exponential phase

label_protocol: Biotinylated cRNA were prepared from 2 micrograms polyA RNA using the BioArray HighYield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY).

extract_protocol: Standard phenol-chloroform extraction from Schmitt, et al. (1990) Nucl. Acids Res, 18:3091-3092.  PolyA RNA isolated using Oligotex mRNA kit from Qiagen.

tag: Medium

value: complete synthetic medium with 2% glucose


title: [GAR+] sample #2

description: [GAR+] W303 yeast grown in 2% glucose medium to late exponential phase.


title: [GAR+] sample #3


title: [gar-] sample #3


title: [gar-] sample #1

source_name: planktonic yeast, late exponential growth phase

value: complete synthetic medium containing 2% glucose


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample Y7

status: Public on Jan 31 2009

first: Andrew

middle: M

last: Sharkey

address: Tennis Court Rd

department: Pathology

institute: University of Cambridge

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample Y7, and was treated with the NK conditioned medium. it is paired with sample G7 (cells from the same patient, but treated wit control medium)

hyb_protocol: The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al. Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

scan_protocol: The fluorescence signal on the microarrays was acquired by using a Genepix 4100 microarray scanner (Axon Instruments, Foster City, CA). The scanned images were processed using GenePix Pro 3.0 software (Axon Instruments).

data_processing: The raw data was normalized per spot and per chip using GeneSpring v7.0 software with intensity dependent (Lowess) normalization (percent of the data used for smoothing 10%) and per chip normalized to 50th percentile. Low hybridisation signals were removed to give an average of 10,000 different RNA transcripts expressed above background. For each cDNA spot on the array, a ratio was derived in which the signal from the test sample (stromal cells treated either with uNK conditioned medium or control medium and labelled with Cy5) was expressed relative to the hybridisation signal in the Cy3-labelled common reference sample hybridised to the array at the same time.The Value in the data is the log of this (test/reference ratio) for each spot on the array.

source_name: Human endometrial stromal cells

label_protocol:
A batch of common reference sample, produced by pooling RNA from all stromal cells treated with control medium was labelled in the same way with Cy3 (common reference sample).
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.
18.
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

extract_protocol: RNA isolation was performed using the TRIZOL method followed by purification with the High Pure RNA Isolation Kits (Roche Diagnostics, Mannheim, Germany) for DNA digestion. Total RNA was isolated rfrom 7 patients and pooled to give a reference RNA

treatment_protocol: Human endometrial stromal cells grown in normal medium (untreated control). Pooled common reference sample

tag: Human endometrial stromal cells were cultured in vitro, and treated with control medium. Total RNA was isolated from 7 different patients, pooled and labelled with Cy3. This is the refence sample used in channel 1. All test samples in this experiment were hybridised against this common reference

source_name: Human endometrial stromal cells patient Y7

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient Y7
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

treatment_protocol: Human endometrial stromal cells from patient Y7 were grown in medium conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient Y7 were cultured in vitro, and treated with medium conditioned by uterine NK cells. Total RNA was isolated and labelled with Cy5


title: [GAR+] sample #1


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample G3

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample G3, and was treated with the control medium. it is paired with sample Y3 (cells from the same patient, but treated with NK cells conditioned medium medium)

source_name: Human endometrial stromal cells patient G3

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient G3
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

extract_protocol: RNA isolation was performed using the TRIZOL method followed by purification with the High Pure RNA Isolation Kits (Roche Diagnostics, Mannheim, Germany) for DNA digestion.

treatment_protocol: Human endometrial stromal cells from patient G3 were grown in control medium NOT conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient G3 were cultured in vitro, and treated with control medium (not conditioned by NK cells). Total RNA was isolated and labelled with Cy5


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample G5

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample G5, and was treated with the control medium. it is paired with sample Y5 (cells from the same patient, but treated with NK cells conditioned medium medium)

source_name: Human endometrial stromal cells patient G5

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient G5
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

treatment_protocol: Human endometrial stromal cells from patient G5 were grown in control medium NOT conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient G5 were cultured in vitro, and treated with control medium (not conditioned by NK cells). Total RNA was isolated and labelled with Cy5


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample G4

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample G4, and was treated with the control medium. it is paired with sample Y4 (cells from the same patient, but treated with NK cells conditioned medium medium)

source_name: Human endometrial stromal cells patient G4

treatment_protocol: Human endometrial stromal cells from patient G4 were grown in control medium NOT conditioned for 24 hours previously by culture of uterine NK cells


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample G7

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample G7, and was treated with the control medium. it is paired with sample Y7 (cells from the same patient, but treated with NK cells conditioned medium medium)

source_name: Human endometrial stromal cells patient G7

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient G7
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

treatment_protocol: Human endometrial stromal cells from patient G7 were grown in control medium NOT conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient G7 were cultured in vitro, and treated with control medium (not conditioned by NK cells). Total RNA was isolated and labelled with Cy5


title: Normal kidney, 12 weeks old fetus [HG-U133A]

description: Gene expression data for normal kidney

source_name: 12 weeks old normal renal tissue


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample G6

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample G6, and was treated with the control medium. it is paired with sample Y6 (cells from the same patient, but treated with NK cells conditioned medium medium)

source_name: Human endometrial stromal cells patient G6

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient G6
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

treatment_protocol: Human endometrial stromal cells from patient G6 were grown in control medium NOT conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient G6 were cultured in vitro, and treated with control medium (not conditioned by NK cells). Total RNA was isolated and labelled with Cy5


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample G2

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample G2, and was treated with the control medium. it is paired with sample Y2 (cells from the same patient, but treated with NK cells conditioned medium medium)

source_name: Human endometrial stromal cells patient G2

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient G2
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

treatment_protocol: Human endometrial stromal cells from patient G2 were grown in control medium NOT conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient G2 were cultured in vitro, and treated with control medium (not conditioned by NK cells). Total RNA was isolated and labelled with Cy5


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample Y5

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample Y5, and was treated with the NK conditioned medium. it is paired with sample G5 (cells from the same patient, but treated wit control medium)

source_name: Human endometrial stromal cells patient Y5

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient Y5
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

treatment_protocol: Human endometrial stromal cells from patient Y5 were grown in medium conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient Y5 were cultured in vitro, and treated with medium conditioned by uterine NK cells. Total RNA was isolated and labelled with Cy5


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample Y6

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample Y6, and was treated with the NK conditioned medium. it is paired with sample G6 (cells from the same patient, but treated wit control medium)

source_name: Human endometrial stromal cells patient Y6

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient Y6
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

treatment_protocol: Human endometrial stromal cells from patient Y6 were grown in medium conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient Y6 were cultured in vitro, and treated with medium conditioned by uterine NK cells. Total RNA was isolated and labelled with Cy5


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample Y4

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample Y4, and was treated with the NK conditioned medium. it is paired with sample G4 (cells from the same patient, but treated wit control medium)

source_name: Human endometrial stromal cells patient Y4

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient Y4
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

treatment_protocol: Human endometrial stromal cells from patient Y4 were grown in medium conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient Y4 were cultured in vitro, and treated with medium conditioned by uterine NK cells. Total RNA was isolated and labelled with Cy5


title: HDAC8 KD, No R1881, rep1

status: Public on Jan 01 2009

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data was analyzed using GeneSpring. Gene with intensity >250 either unstimulated or stimulated with R1881 was included for analysis. Data was normaled by medium of the chip. No per gene normalization was performed.

source_name: LNCaP Cells

label_protocol: standard Affymetrix protocol

growth_protocol: LNCaP cells were grown in charcoal stripped medium

extract_protocol: RNAeasy Kit

treatment_protocol: As per title for 16 hours, all in the presence of cyclohexamide


title: HDAC2 KD, 1nM R1881, rep2


title: HDAC3 KD, 1nM R1881, rep2


title: HDAC3 KD, No R1881, rep1


title: HDAC8 KD, 1nM R1881, rep2


title: HDAC8 KD, 1nM R1881, rep1


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample Y2

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample Y2, and was treated with the NK conditioned medium. it is paired with sample G2 (cells from the same patient, but treated wit control medium)

extract_protocol: RNA isolation was performed  using the TRIZOL method followed by purification with the High Pure RNA Isolation Kits (Roche Diagnostics, Mannheim, Germany) for DNA digestion. Total RNA was isolated rfrom 7 patients and pooled to give a reference RNA

source_name: Human endometrial stromal cells patient Y2

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient Y2
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

treatment_protocol: Human endometrial stromal cells from patient Y2 were grown in medium conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient Y2 were cultured in vitro, and treated with medium conditioned by uterine NK cells. Total RNA was isolated and labelled with Cy5


title: HDAC8 KD, No R1881, rep2


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample Y3

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample Y3, and was treated with the NK conditioned medium. it is paired with sample G3 (cells from the same patient, but treated wit control medium)

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient Y3
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

treatment_protocol: Human endometrial stromal cells from patient Y3 were grown in medium conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient Y3 were cultured in vitro, and treated with medium conditioned by uterine NK cells. Total RNA was isolated and labelled with Cy5


title: 200 vs 100 microns depth biofilm

status: Public on Jan 16 2009

city: Jerusalem

first: Moshe

last: Shemesh

address: Hebrew University-Hadassah POB 12272

department: Institute of Dental Sciences

country: Israel

institute: Hebrew University-Hadassah

description: 200 vs 100 microns depth biofilm

hyb_protocol: Each Cy3-labeled sample was mixed with equal amount of Cy5-labeled sample, and the mixtures were allowed to dry in a speed vacuum for about 1 hour. The hybridization was performed basically according to TIGR protocol (http://pfgrc.tigr.org/protocols/M008.pdf). The samples were resuspended in hybridization buffer containing: 50% formamide, 5 x SSC, 0.1% SDS and 20µg yeast tRNA, and heated at 90°C for 10 min. following a quick centrifugation, the Cy dye-coupled probes were applied to microarray slides and incubated over-night at 42°C. The hybridization was carried out in corning hybridization chambers submerged in a water bath.

scan_protocol: The hybridized slides were washed and scanned by using Axon GenePix 4000B Scanner (Axon Instruments, Foster City, CA) with adjusted settings in order to obtain a similar green and red overall intensity.

data_processing:
The hybridization patterns and intensities were quantitatively analyzed using the GenePix Pro 4.0 software (Axon) on scanned microarray images.
The result files (gpr) produced by GenePix have been analyzed utilizing LIMMA (Smyth, 2004) software package, available from CRAN site (http://www.r-project.org). Spots flagged as not found or absent in GenePix were removed by filtering. Another filter was applied for saturated spots. After filtering, the data within the same slide was normalized using global loess normalization with the default smoothing span of 0.3 (Smyth and Speed, 2003) To identify differentially expressed genes, a parametric empirical Bayesian approach implemented in LIMMA was used (Lonnstedt and Speed, 2002). A moderated t test was performed in parallel, with the use of a false discovery rate (Reiner et al., 2003) correction for multiple testing. As TIGR arrays include four replicates for each gene, we used the duplicate Correlation function (Smyth et al., 2005) available in LIMMA to acquire an approximation of gene-by-gene variance. This method greatly improves the precision with which the gene-wise variances are estimated and thereby maximize inference methods designed to identify differentially expressed genes. P value <0.05 confidence level has been used to pinpoint those significantly differentiated genes.

organism: Streptococcus mutans

source_name: 200 microns depth biofilm

label_protocol: Synthesis of cDNA and labeling was performed as describes in http://pfgrc.tigr.org/protocols/M007.pdf as follows: cDNA was generated with random hexamers (6µg) from 2µg total RNA using the superscript III reverse transcriptase (Invitrogen). The reverse transcription reaction was carried out at 42°C overnight with aminoallyl labeled dUTP. Removal of unincorporated aa-dUTP and free amines was carried out using Microcon YM-30 (Millipore) filters according to manufacturer recommendations. Coupling of aminoallyl-labelled cDNA to Cy-dye esters was preformed in 0.1M sodium carbonate buffer pH 8.6 for 1 hr at room temperature. Removal of free dyes was accomplished with the Qiagen QIAquick PCR purification columns. The labeling level was the quantified using a spectrophotometer ND-100 (Nanodrop Technologies).

extract_protocol: RNA extraction from biofilm grown cells was performed as follows: biofilm-grown S. mutans cells were suspended in TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) and dislodged by scraping into a 2-ml microcentrifuge tube containing 0.4 ml 1-mm-diameter glass beads (Sigma-Aldrich). The cells were disrupted with the aid of a Fast Prep Cell Disrupter (Bio 101, Savant Instruments, Inc., NY, USA), centrifuged and the RNA containing supernatant was supplemented with 1-Bromo-3-Chloropropane (BCP) (Molecular Research Center, Cincinnati, OH, USA). The upper aqueous phase was precipitated with isopropanol. After centrifugation, the resulting RNA pellet was washed with ethanol and resuspended in diethyl pyrocarbonate (DEPC)-treated water. Because of the sensitivity of the PCR, residual contaminating DNA was eliminated by incubation of the sample with RNase-free DNase (Promega, Madison, WI, USA). The RNA concentration was determined spectrophotometrically using the Nanodrop Instrument (ND-1000, Nanodrop Technologies, Wilmington, DE, USA). The integrity of the RNA was assessed by agarose-gel electrophoresis.

tag: Biofilm of Streptococcus mutans UA159 grown to 200-microns depth

source_name: 100 microns depth biofilm

tag: Biofilm of Streptococcus mutans UA159 grown to 100-microns depth


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample G1

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample G1, and was treated with the control medium. it is paired with sample Y1 (cells from the same patient, but treated with NK cells conditioned medium medium)

source_name: Human endometrial stromal cells patient G1

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient G1
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

treatment_protocol: Human endometrial stromal cells from patient G1 were grown in control medium NOT conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient G1 were cultured in vitro, and treated with control medium (not conditioned by NK cells). Total RNA was isolated and labelled with Cy5


title: HDAC3 KD, 1nM R1881, rep1


title: 100 vs 400 microns depth biofilm_2

description: 100 vs 400 microns depth biofilm_2

source_name: biofilm of 100 microns depth

source_name: biofilm of 400 microns depth

extract_protocol: biofilm-grown S. mutans cells were suspended in TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) and dislodged by scraping into a 2-ml microcentrifuge tube containing 0.4 ml 1-mm-diameter glass beads (Sigma-Aldrich). The cells were disrupted with the aid of a Fast Prep Cell Disrupter (Bio 101, Savant Instruments, Inc., NY, USA), centrifuged and the RNA containing supernatant was supplemented with 1-Bromo-3-Chloropropane (BCP) (Molecular Research Center, Cincinnati, OH, USA). The upper aqueous phase was precipitated with isopropanol. After centrifugation, the resulting RNA pellet was washed with ethanol and resuspended in diethyl pyrocarbonate (DEPC)-treated water. Because of the sensitivity of the PCR, residual contaminating DNA was eliminated by incubation of the sample with RNase-free DNase (Promega, Madison, WI, USA). The RNA concentration was determined spectrophotometrically using the Nanodrop Instrument (ND-1000, Nanodrop Technologies, Wilmington, DE, USA). The integrity of the RNA was assessed by agarose-gel electrophoresis.

tag: Biofilm of Streptococcus mutans UA159 grown to 400-microns depth


title: 400 vs 100 microns depth biofilm

description: 400 vs 100 microns depth biofilm

tag: biofilm of Streptococcus mutans UA159 grown in 400-microns depth

tag: biofilm of Streptococcus mutans UA159 grown in 100-microns depth


title: HDAC1 KD, 1nM R1881, rep2


title: HDAC2 KD, No R1881, rep2


title: HDAC2 KD, 1nM R1881, rep1


title: Luciferase KD, 1nM R1881, rep2


title: 100 vs 400 microns depth biofilm_1

description: 100 vs 400 microns depth biofilm_1


title: Luciferase KD, 1nM R1881, rep1


title: HDAC3 KD, No R1881, rep2


title: Uterine stromal cell_cultured with uNK conditioned Medium_ sample Y1

description: The endometrial stromal cells from several individuals were grown separately and each treated with the same batch of conditioned medium to assess the responses of stromal cells from different patients. This Patient is sample Y1, and was treated with the NK conditioned medium. it is paired with sample G1 (cells from the same patient, but treated wit control medium)

source_name: Human endometrial stromal cells

tag: Human endometrial stromal cells were cultured in vitro, and treated with control medium. Total RNA was isolated from 7 different patients, pooled and labelled with Cy3. This is the refence sample used in channel 1. All test samples in this experiment were hybridised against this common reference

label_protocol:
The generation of the amplified labelled cDNA targets and the chip hybridization was performed using the method of Petalidis et al.using RNA from patient Y1
Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003;31:e142.

extract_protocol: RNA isolation was performed  using the TRIZOL method followed by purification with the High Pure RNA Isolation Kits (Roche Diagnostics, Mannheim, Germany) for DNA digestion.

treatment_protocol: Human endometrial stromal cells from patient Y1 were grown in medium conditioned for 24 hours previously by culture of uterine NK cells

tag: Human endometrial stromal cells from patient Y1 were cultured in vitro, and treated with medium conditioned by uterine NK cells. Total RNA was isolated and labelled with Cy5


title: HDAC1 KD, 1nM R1881, rep1


title: HDAC1 KD, No R1881, rep1


title: 100 vs 200 microns depth biofilm

description: 100 vs 200 microns depth biofilm


title: Luciferase KD, No R1881, rep1


title: HDAC2 KD, No R1881, rep1


title: Luciferase KD, No R1881, rep2


title: HLE cells stimulated with AFP

status: Public on Dec 31 2008

city: Chiba

first: Noboru

last: Mitsuhashi

address: 1-33 Yayoi-cho, Inage-ku

department: Section for Medical Nanotechniques

institute: Research Center for Frontier Medical Engineering, Chiba University

description: HLE cell line

hyb_protocol: Agilent two-color gene expression hybridization/wash protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 micron resolution. Images were quantified using Agilent Feature Extraction software version 9.5.3

data_processing: LOWESS normalized, background-subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Control HLE cells, untreated

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol.

growth_protocol: HepG2 cells were cultured in Dulbecco's Modified Eagle's Medium containg 10% fetal bovine serum. HLE cells were cultured in Dulbecco's Modified Eagle's Medium containg 10% fetal bovine serum.

extract_protocol: Total RNA extracted using Rneasy (Qiagen) following manufacturer's instructions.

treatment_protocol: Five million HepG2 cells were cultured with or without 5,000 ng/ml of human cord blood AFP for 24 hours. Five million HLE cells were cultured with or without 5,000 ng/ml of human cord blood AFP for 24 hours.

tag: HLE cells were cultured without 5,000 ng/ml of human cord blood AFP for 24 hours.

source_name: HLE cells stimulated with AFP

tag: HLE cells were cultured with 5,000 ng/ml of human cord blood AFP for 24 hours.


title: Averaged 2021_1 ... 2021_4

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

institute: Uniklinikum Giessen

description: no additional information required

hyb_protocol: Labeled cDNAs were hybridized in Agilent in-situ hybridization buffer overnight at 60°C. Slides were mounted in Agilent hybridization chambers that were kept rotating at 10 rpm in an hybridization oven. Hybridization and subsequent washing and drying of the slides were performed following the Agilent hybridization protocol.

scan_protocol: Dried slides were scanned using the GenePix 4100A scanner (Axon Instruments). Photomultiplier tube gains were adjusted to get about 1% spots with saturated pixels and similar intensity histograms in both channels.

data_processing: Data were evaluated using the R software (http://www.R-project.org) and the limma package from BioConductor (Gentleman R 2004 Genome Biol 5(10):R80, Smyth GK 2004 Stat Appl Genet Mol Biol 3:Article3). The spots were weighted for subsequent analyses according to the spot intensity, homogeneity, and saturation. The spot intensities were corrected for the local background using the method of Edwards with an offset of 64 to stabilize the variance of low-intensity spots. The M/A data were LOESS normalized before averaging. Genes were ranked for differential expression using a moderated t-statistic. Candidate lists were created by adjusting the false-discovery rate to 10 %.

source_name: PBM

label_protocol: Purified total RNA was amplified and Cy-labeled using the SMART™ kit (Clontech BD Healthcare) following the kit instructions with 24 amplification cycles. Monoreactive CyDyes (Amersham) were coupled in subsequent 4 cycles.

growth_protocol: Mice were kept under specified pathogen free conditions with free access to water and food.

extract_protocol: Total cellular RNA was isolated from 30.000-40.000 freshly sorted GFP-positive MPs using the RNeasy Micro kit. RNA was eluted in 12 μl RNase free H2O. RNA was quantified spectrophotometrically (Nanodrop ND-100) and the quality was assessed by the 18S/28S-rRNA bands in capillary electrophoresis (Bioanalyzer 2100, Agilent Biosystems).

treatment_protocol:
Mice were anesthetized with tetrazoline hydrochloride and ketamine, and the trachea was exposed. Subsequently, catheter (Abbot, Wiesbaden, Germany) was inserted into trachea and Pam3CSK4 (50 µg/mouse dissolved in total volume of 60 µl) was installed under stereomicroscopic control (Leica MS5, Wetzlar, Germany). After installation, wounds were closed and mice were allowed to recover with free access to food and water.
24 h post-challenge, mice were sacrificed with an overdose of isoflurane (Forene; Abbott, Wiesbaden, Germany) and blood and BAL fluid (BALF) collection was done as describe previously (Srivastava 2005 J Immunol 175(3):1884-93; Steinmuller 2006 Respir Res 7:30).
Blood was collected from the vena cava inferior. The lysis of red blood cells was performed using ammonium chloride solution.
Prior to cell sorting, samples were filtered through a 40 µm cell strainer.

tag: Cells

value: Peripheral Blood Monocytes

tag: Isolation

value: FACS from broncho-alvoelar lavage (24h post challange)

tag: Animals

value: CX3CR1GFP/GFP mice on a mixed C57BL/6 x 129/Ola background

tag: Age

value: 8 - 12 weeks

tag: Gender

value: Mixed

tag: Treatment

value: i.t. application of 50 µg TLR2 ligand Pam3CSK4

source_name: AM

treatment_protocol:
Mice were anesthetized with tetrazoline hydrochloride and ketamine, and the trachea was exposed. Subsequently, catheter (Abbot, Wiesbaden, Germany) was inserted into trachea and Pam3CSK4 (50 µg/mouse dissolved in total volume of 60 µl) was installed under stereomicroscopic control (Leica MS5, Wetzlar, Germany). After installation, wounds were closed and mice were allowed to recover with free access to food and water.
24 h post-challenge, mice were sacrificed with an overdose of isoflurane (Forene; Abbott, Wiesbaden, Germany) and blood and BAL fluid (BALF) collection was done as describe previously (Srivastava 2005 J Immunol 175(3):1884-93; Steinmuller 2006 Respir Res 7:30).
Blood was collected from the vena cava inferior. The lysis of red blood cells was performed using ammonium chloride solution.
Trachea was exposed and a small incision was made to insert a shortened 21-gauge cannula connected to a 1-ml insulin syringe, followed by repeated i.t. instillations of 0.5 ml aliquots of PBS (pH 7,2, supplemented with 2 mM EDTA). BAL was performed until a total volume of 5 ml was recovered. BALF was spun for 10 min at 1400 rpm at 4°C and cells were dissolved in 1 ml of RPMI 1640 medium containing 10 % FCS and L-glutamine. Recovered BAL and blood cells were pooled from 10-12 CX3CR1GFP/+ mice to obtain sufficient cell numbers for flow sorting.
Prior to cell sorting, samples were filtered through a 40 µm cell strainer.

value: Alveolar Macrophages

value: FACS from broncho-alvoelar lavage (BAL) (24h post challenge)


title: wild-type strain_CS medium_1

first: Taisuke

last: Wakamatsu

address: Machikaneyama 1-1

department: Department of Biology

institute: Osaka University

description: wild-type strain_CS medium_1

hyb_protocol: 3’-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401 GeneChip (Affymetrix, Santa Clara, CA). The array was incubated for 16 h at 50oC in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 1 mg of herring sperm DNA (Promega), 0.5 mg of bovine serum albumin (BSA), the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix), and then the array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneArray Scanner (Affymetrix).

data_processing: The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.0 (Affymetrix, Santa Clara, CA).

source_name: wild-type strain_CS medium_1

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen). The cDNA was fragmented with 35 units of DNase I (GE Healthcare Bio-Science Corp.) at 37oC for 10 min, and after inactivation at 98oC for 10 min, the cDNA fragments were labeled with biotin-dideoxy UTP, using terminal transferase according to the manufacturer’s instructions (ENZO Biochem. Inc., Farmingdale, NY).

growth_protocol: The T. thermophilus HB8 TTHA0118 deletion mutant strain was pre-cultured at 70oC in 4 ml of TT medium containing 0.4% polypeptone, 0.2% yeast extract, 0.1% NaCl, 0.4 mM MgCl2,and 0.4 mM CaCl2, which was adjusted to pH 7.3 with NaOH. When the cell density of thel preculture reached 1.5 × 10^7 cells/ml, 250-micro l of culture was inoculated into 100 ml fresh CS medium containing 2% Sucrose, 2% sodium glutamate, 0.055% K2HPO4, 0.018% KH2PO4, 0.2% NaCl, 0.05% (NH4)2SO4, 0.0125% MgCl2 6H2O, 0.0025% CaCl2 2H2O, 0.001% FeSO4 7H2O, 0.00012% NaMoO3 2H2O, 0.00001% VOSO4 xH2O, 0.00005% MnCl2 4H2O, 0.000006% ZnSO4 7H2O, 0.0000015% 5H2O, 0.00008% CoCl2 6H2O, 0.000002% NiCl2 2H2O, 0.001% Biotin, and 0.01% Thiamin which was adjusted to pH 7.3 with NaOH. The cells were cultured at 70oC and harvested at 7× 10^8 cells/ml.

extract_protocol: Crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol to the cell pellet. This mixture was incubated at 65oC for 5 min, chilled on ice for 5 min, and then centrifuged at 4oC. Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase. After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform. The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol. The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 40 micro l of water. The RNA was treated with DNase I (Ambion, Austin, TX) at 37oC for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70oC for 5 min. Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

treatment_protocol: The 50 ml of culture was centrifuged by 7000 rpm, 4oC, and 10 minutes. After the removal of supernatant, cell pellet was frozen by using liquid nitrogen.

tag: wild-type strain at 7 × 10^8 cells/ml on CS medium


city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

description: Gene expression data from generation 230 of E. coli grown in LB broth with 10% cranberry juice

hyb_protocol: The cocktail was hybridized onto the Affymetrix GeneChip E. coli Genome 2.0 arrays,  which contains probe sets for 20,366 genes of  Escherichia coli. Hybridization was carried out for 16 h at 45 °C with rotation at 60 rpm. The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip Scanner 3000.

scan_protocol: The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip Scanner 3000.   GeneChip Operating Software 1.2 (GCOS 1.2) (Affymetrix) was used to acquire and process array images, determine the quantity and presence or absence of a transcript using the Microarray Suite 5.0 (MAS5) algorithm, and generated the Report files summarizing the quality of target detection for each microarray.

data_processing:
CEL files were processed using the Bioconductor affy package. Because the second control array had significantly lower expression values, we ran two concurrent sets of analyses, one using all of the CEL files, and the other omitting the Control_2 CEL file.  (Files and results using the latter were given the suffix 14, since only 14 of the 15 CEL files were used.) In each case, MAS5, RMA, Li and Wong's MBEI (used in the dChip software package) and Huber's VSN (variance stabilizing normalization) gene expression values were obtained.  Using the Bioconductor limma package, the top 50 differentially expressed genes (all treatments relative to the control arrays) were obtained for each the expression methodologies.  Genes were then given an overall ranking based on their ranks within the various expression types.  More specifically,a gene was assigned the median of its ranks within the tables of expression methodolgies.
VALUE = MAS5.0 signal intensity, RMA = Izarry's Robust Multichip Analysis, VSN = Huber's Variance Stabilization Normalization, MBEI = Li & Wong's Model Based Expression Index (aka dChip), VSN14 = VSN with Control_2 dropped, MBEI14 = MBEI with Control_2 dropped.  All expression values were obtained using Bioconductor's affy package.  MAS5.0_14 and RMA14 values are not included since the MAS5 and RMA values are the same with Control_2 present and absent. VSN14 and MBE14 values were not determined for Control_2, since Control_2 was excluded from the calculations of VSN14 and MBE14.

organism: Escherichia coli

source_name: ATCC 35218, Generation 230 E. coli grown in LB broth + 10% cranberry juice, rep 1

label_protocol: Target Preparation and Hybridization to Arrays: 10 µg of total RNA contained RNA controls with known concentrations to monitor the quality of the procedures were transcribed to cDNAs using SuperScript II reverse transcriptase with random primers (Invitrogen Corp., Carlsbad, CA).  The first strand cDNAs synthesis was carried out at 25oC for 10 minutes, 37oC for 1 hour, then 42oC for 1 hour.  The cDNA was fragmented by DNase I and labeled with GeneChip® DNA labeling reagent and terminal deoxynucleotide transferase (Affymetrix) as described in the GeneChip Expression Analysis Technical Manual version 701029 Rev. 4 (Affymetrix).

growth_protocol: Batch cultures of E. coli were grown in 50 mL polypropylene centrifuge tubes containing 12 mL of growth media and were incubated at 37°C with 250 rpm agitation.   Diploid strains MLY61 a/alpha (ura3-52/ura3-52 MATa/alpha) and MLY132 a/alpha (delta gpa2::G418/delta gpa2::G418 ura3-52/ura3-52 MATa/alpha) were obtained from J. Heitman, Duke University{Lorenz, 2000 #19; Lorenz, 1997 #33}. Standard YPM media were used as described{Sherman, 1991 #36}. Synthetic low ammonium media consisting of SLAM (0.17% Yeast Nitrogen Base without ammonium sulfate or amino acids, 50 µM ammonium sulfate, 2% maltose) were used when switching to low nitrogen pseudohyphal inducing conditions{Lorenz, 2000 #19; Lorenz, 1997 #33}. Similar to a previously described method{Pan, 2000 #37}, strains were grown to an OD600 of 1.0 in YPM media. Approximately 200 OD600 units were collected by filtering followed by resuspension in 10 mL RNAlater (Ambion) for <30 min, pelleted by centrifugation, flash frozen and stored at –80 °C. Strains were also grown to an OD600 of 1.0 in YPM media and approximately 200 O.D. were collected by filtration and transferred to SLAM media for 2 h at 30 °C prior to collection as above.

extract_protocol: Total RNA were extracted using RNeasy Protect Bacteria Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer's instructions  RNA Isolation: The RibopureTM-Yeast kit (Ambion) was used to extract total RNA from yeast cells. Briefly, for each RNAlater-treated sample, cells were pelleted in a microtube and any remaining RNAlater removed. Then lysis buffer, 10% SDS, and 25:24:1 phenol:chloroform:isoamyl alcohol were used to resuspend the pellet, and the mixture was transferred to a screw cap microtube with Zirconia beads (BioSpec Products) to disrupt the yeast cells by vortexing. The lysate was centrifuged, and the upper aqueous layer transferred to 15 mL conical tubes with Binding Buffer and 100% ethanol. The mixture was drawn through a filter cartridge to capture the RNA, followed by washing and elution. To remove contaminating DNA, 50 µL of the eluted RNA was treated with 10 µL of 10X DNase I buffer and 4 µL of 8 units µL-1 DNase I. The reaction was mixed, incubated at 37 °C for 30 min, followed by addition of 0.1 volume DNase Inactivation Reagent. After 5 min at room temperature, the mixture was spun through a spin column (Qiagen) to remove the DNase binding beads in the DNase Inactivation Reagent. The quality/quantity of purified yeast total RNA was determined by separating 1 µL from each sample on a Bioanalyzer 2100 (Agilent).

treatment_protocol: Juice-spiked broth was prepared through the addition of filter sterilized Mountain Sun 100% Cranberry Juice (neutralized to pH 7.4 through addition of sodium hydroxide) to concentrated LB broth.  The final juice concentration in the growth media was 10%.


title: HDAC1 KD, No R1881, rep2


description: Gene expression data from generation 210 of E. coli grown in LB broth with 10% cranberry juice

source_name: ATCC 35218, Generation 210 E. coli grown in LB broth + 10% cranberry juice, rep 1


source_name: ATCC 35218, Generation 210 E. coli grown in LB broth + 10% cranberry juice, rep 2


source_name: ATCC 35218, Generation 230 E. coli grown in LB broth + 10% cranberry juice, rep 3


title: TTHA0118 deletion mutant strain_CS medium_3

tag: TTHA0118 deletion mutant strain at 7 × 10^8  cells/ml on CS medium


title: E. coli grown in LB, rep2

description: Gene expression data from E. coli grown in LB broth

source_name: ATCC 35218, E. coli grown in LB, rep2

tag: E. coli grown in LB, rep2


description: Gene expression data from generation 50 of E. coli grown in LB broth with 10% cranberry juice

source_name: ATCC 35218, Generation 50 E. coli grown in LB broth + 10% cranberry juice, rep 3


source_name: ATCC 35218, Generation 50 E. coli grown in LB broth + 10% cranberry juice, rep 1


source_name: ATCC 35218, Generation 210 E. coli grown in LB broth + 10% cranberry juice, rep 3


title: TTHA0118 deletion mutant strain_CS medium_2


description: Gene expression data from generation 160 of E. coli grown in LB broth with 10% cranberry juice

source_name: ATCC 35218, Generation 160 E. coli grown in LB broth + 10% cranberry juice, rep 3


source_name: ATCC 35218, Generation 160 E. coli grown in LB broth + 10% cranberry juice, rep 2


title: TTHA0118 deletion mutant strain_CS medium_4


title: TTHA0118 deletion mutant strain_CS medium_1


title: wild-type strain_CS medium_4

description: wild-type strain_CS medium_4

source_name: wild-type strain_CS medium_4


source_name: ATCC 35218, Generation 230 E. coli grown in LB broth + 10% cranberry juice, rep 2


title: E. coli grown in LB, rep3

source_name: ATCC 35218, E. coli grown in LB, rep3

tag: E. coli grown in LB, rep3


title: ARF-129

type: genomic

city: Philadelphia

first: JIANMING

last: PEI

state: PA

address: 333 Cottman Ave.

department: Population Science

institute: Fox Chase Cancer Center

description: Comparative genomic hybridization

hyb_protocol: Appropriate cyanine 5- and cyanine 3-labeled DNA sample pairs were combined and then mixed with mouse Cot-1 DNA, Agilent 10X Blocking Agent, and Agilent 2X Hybridization Buffer. The labeled target solution was hybridized to Agilent’s 244K Mouse Genome CGH microarray (G4415A) using SureHyb chambers. After hybridization the microarrays were washed and dried according to the procedures described in Agilent’s protocol.

scan_protocol: Microarray slides were scanned immediately using an Agilent microarray scanner.

data_processing: Data for individual features on the microarray were extracted from the scan image using Agilent’s Feature Extraction (FE) Software. Output files from FE were subsequently imported into Agilent’s CGH data analysis software, CGH Analytics, for DNA copy number analysis.

molecule: genomic DNA

source_name: ARF-129, primary malignant mesothelioma cells

label_protocol: In brief, 3 ug of genomic DNA was digested with AluI and RsaI. Digested DNA was labeled using an Agilent Genomic DNA Labeling Kit PLUS.  Test and reference DNA samples were labeled with either cyanine 5- or cyanine 3-dUTP, according to the manufacturer’s protocol. Labeled DNA products were purified using Microcon YM-30 filtration units (Millipore), and DNA yield and dye incorporation were determined using an ND-1000 spectrophotometer (NanoDrop).

extract_protocol: Genomic DNA was isolated using Puregene Genomic DNA Purification Kit (D-5500A) according to the manufacturer's protocol.

tag: MM fr het mouse; Sherr strain (not backcrossed)

extract_protocol: DNA samples were obtained from Jackson Laboratories.

tag: Reference


title: wild-type strain_CS medium_2

description: wild-type strain_CS medium_2

source_name: wild-type strain_CS medium_2


title: wild-type strain_CS medium_3

description: wild-type strain_CS medium_3

source_name: wild-type strain_CS medium_3


source_name: ATCC 35218, Generation 50 E. coli grown in LB broth + 10% cranberry juice, rep 2


source_name: ATCC 35218, Generation 160 E. coli grown in LB broth + 10% cranberry juice, rep 1


title: HepG2 cells stimulated with AFP

description: HepG2 cell line

source_name: Control HepG2 cells, untreated

tag: HepG2 cells were cultured without 5,000 ng/ml of human cord blood AFP for 24 hours.

source_name: HepG2 cells stimulated with AFP

tag: HepG2 cells were cultured with 5,000 ng/ml of human cord blood AFP for 24 hours.


title: HAEC cells rep 3

city: Baltimore

middle: N

last: Grigoryev

state: MD

institute: JHU

description: The basic Illumina data is returned from the scanner in the form of an “.idat” file which contains single intensity data values/gene following the computation of a trimmed mean average for each probe type represented by a variable number of bead probes/gene on the array.  The Bead Studio software returns information on the number and standard deviation of all the bead measurements per probe/gene as well as a detection call based on a comparison between the measured intensity calculated for a single probe/gene and the intensities measured for a large number of negative control beads built-in to the BeadChip arrays (D = %above negative/100, 1 = perfect, i.e. the intensity value of a gene is greater than all the intensities for every negative control tested).

hyb_protocol: Illumina

scan_protocol: Preliminary analysis of the scanned data was performed using Illumina BeadStudio software.

data_processing: The Array hybridization signal analysis was adapted for Illumina platform from previously reported method for Affymetrix [Grigoryev et al.  Identification of candidate genes in scleroderma-related pulmonary arterial hypertension. Transl Res (In press).]  The significance of hybridization signals was tested for “Present” or “Absent” transcript characteristic.  The detectable genes were those with BeadStudio identification ratio >0.95.  The chip background and brightness for all 12 samples were computed using high quartile and whole set of “Absent” hybridization signals, respectively.  The expression data was stratified by experimental conditions (n=4) and hybridization of each transcript was evaluated.  The transcripts that were called detectable (Present) by BeadStudio and produced signal at least twice as high as that of a background in at least 3 out of 4 hybridizations in any given experimental condition were considered expressed in the given condition. The signal intensity values of these transcripts from each chip were increased by corresponding to a given chip background value (background adjustment) and divided by a chip brightness coefficient (normalization).

label: Illumina

source_name: human cells

label_protocol: RNA samples was labeled according to the chip manufacturers recommended protocols.  In brief, for Illumina, 0.5 µg of total RNA from each sample was labeled by using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX 78744-1832, cat. no. IL1791) in a process of cDNA synthesis and in vitro transcription similar to that outlined for Affymetrix above.  Single stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP (Roche Diagnosics GmbH, Mannheim, Germany, cat. no. 11388908910).   0.85 g of biotin-labeled cRNA was hybridized (16 hours) to Illumina’s Sentrix MouseRef-8 Expression BeadChips (Illumina, San Diego, CA 92121-1975).  The hybridized biotinylated cRNA was detected with streptavidin-Cy3 and quantitated using Illumina’s BeadStation 500GX Genetic Analysis Systems scanner.

extract_protocol: Total RNA was extracted using the Trizol Reagent method (Invitrogen, Carlsbad, California 92008, cat. no. 15596-026).  Additional purification was performed on RNAeasy columns (Qiagen, Valencia, CA 913555, cat. no. 74104).  The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: Human Artery Endothelial Cells (HAEC)


title: HAEC cells Chronic Hypoxia rep 1

source_name: human cells chronic hypoxia


title: HAEC cells Chronic Hypoxia rep 4


title: HAEC cells Intermittent Hypoxia rep 2

source_name: human cells intermittent hypoxia


title: ARF-128PlusMinus

description: Comparative genomic hybridization

source_name: ARF-128, primary malignant mesothelioma cells

tag: repeat


title: ARF-112

description: Comparative genomic hybridization

source_name: ARF-112, primary malignant mesothelioma cells


title: ARF-110

description: Comparative genomic hybridization

hyb_protocol: Cyanine 5- and cyanine 3-labeled DNA sample pairs were combined and then mixed with mouse Cot-1 DNA, 10X blocking agent, and 2X hybridization buffer, and then hybridized to CGH microarrays using SureHyb chambers. After hybridization the microarrays were washed and dried according to the procedures described in Agilent’s protocol.

source_name: ARF-110, primary malignant mesothelioma cells

extract_protocol: Genomic DNA was isolated using Puregene Tissue Core Kit (Cat# D-5500A) according to the manufacturer's protocol.


title: ARF-104

description: Comparative genomic hybridization

tag: MM fr wt mouse; Sherr strain (not backcrossed); loss(p16/ARF,p15)


title: HAEC cells rep 1


title: 10_B6-129_ileum_8m_DKO-vs-WT_3

city: Duarte

first: Maria

last: Hahn

state: CA

address: 1500 E. Duarte Rd

department: Biology

institute: City of Hope, Beckman Research Institute

description: MIRA Gpx1/2-KO B6.129 ileum 8 month vs. MIRA control B6.129 ileum 8 month

hyb_protocol: According to Agilent aCGH protocol (http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=52010)

scan_protocol: An Axon GenePix 4000B scanner was used with the following settings: 100% power, 5 µm 2 lines to average and PMT gain for each channel adjusted for each array.

data_processing: Agilent ChIP Analytics 1.3 software, default settings, Lowess normalization

source_name: intestinal epithelium from Gpx1/2-KO mice

label_protocol: Agilent aCGH protocol was followed and 1 µg of amplified MIRA-enriched fragments were labeled

extract_protocol: Standard phenol/chloroform method was used for DNA extraction. The MIRA procedure was as described in Rauch et al., 2006. Cancer Research 66:7939–7947

tag: Mouse strain

value: B6.129. Knockout genes:Gpx1, Gpx2. Phenotype:Inflammatory Bowel diasease. Gender:mixed. Age:8-month-old. Tissue:ileum

source_name: intestinal epithelium from control mice

value: B6.129. Knockout genes:Gpx1 or Gpx2. Phenotype:No intestinal inflammation. Gender:mixed. Age:8-month-old. Tissue:ileum.


title: HAEC cells Intermittent Hypoxia rep 4


title: HAEC cells Intermittent Hypoxia rep 1


title: 24_B6_ileum_8m_WT-H3K27me3-vs-Input

description: ChIp-H3K27me3 Gpx1/2-KO B6 ileum 8 month vs. Input control B6 ileum 8 month

data_processing: Feature extraction and Normalization by Axon’s GenePix v.5.1. The CpG island was considered as positive for H3K27me3 binding if it contained three or more probes with a binding ratio of H3K27me3/Input of more than 2 and a distance between each probe of less than 500 bp.

source_name: intestinal epithelium from control mouse

label_protocol: Agilent aCGH protocol was followed and 1 µg of amplified H3K27me3-enriched fragments were labeled

extract_protocol: ChIp with H3K27me3 antibodies (Upstate) using Upstate ChIp protocol. Genome amplification was performed after elongation of sonicated DNA ends and linker ligation.

value: B6.Knockout genes:Gpx1 or Gpx2. Phenotype:No intestinal inflammation. Gender:male. Age:8-month-old. Tissue:ileum.

label_protocol: Agilent aCGH protocol was followed and 1 µg of amplified Input DNA fragments were labeled

extract_protocol: ChIp Input DNA using Upstate ChIp protocol. Genome amplification was performed after elongation of sonicated DNA ends and linker ligation.


title: 24_B6_ileum_8m_WT-H3K27me3-vs-DKO-H3K27me3

description: ChIp-H3K27me3 Gpx1/2-KO B6 ileum 8 month vs. ChIp-H3K27me3 control B6 ileum 8 month

source_name: intestinal epithelium from Gpx1/2-KO mouse

value: B6.Knockout genes:Gpx1, Gpx2. Phenotype:Inflammatory Bowel diasease. Gender:male. Age:8-month-old. Tissue:ileum


title: 12_B6-129_ileum_28d_DKO-vs-WT

description: MIRA Gpx1/2-KO B6.129 ileum 28 days vs. MIRA control B6.129 ileum 28 days

value: B6.129. Knockout genes:Gpx1, Gpx2. Phenotype:Inflammatory Bowel diasease. Gender:mixed. Age:28-days-old. Tissue:ileum

value: B6.129. Knockout genes:Gpx1 or Gpx2. Phenotype:No intestinal inflammation. Gender:mixed. Age:28-days-old. Tissue:ileum.


title: E. coli grown in LB, rep1

source_name: ATCC 35218, E. coli grown in LB, rep1

tag: E. coli grown in LB, rep1


title: 10_B6-129_ileum_8m_DKO-Tumor#48-vs-WT

description: MIRA Gpx1/2-KO B6.129 Intestinal tumor 8 month vs. MIRA control B6.129 ileum 8 month

source_name: Intestinal tumor from Gpx1/2-KO mouse#48

value: B6.129. Knockout genes:Gpx1, Gpx2. Phenotype:Inflammatory Bowel diasease. Gender:male. Age:8-month-old. Tissue:Intestinal tumor


title: HAEC cells rep 4


title: HAEC cells Chronic Hypoxia rep 3


title: HAEC cells Chronic Hypoxia rep 2


title: 20_B6-129_ileum_WT_28d-vs-8m

description: MIRA control B6.129 ileum 28 days vs. MIRA control B6.129 ileum 8 month

source_name: Intestinal epithelium from control mice

value: B6.129. Knockout genes:Gpx1 or Gpx2. Phenotype:No intestinal inflammation. Gender:male. Age:28-days-old. Tissue:ileum


title: 20_B6_ileum_WT_28d-vs-8m

description: MIRA control B6 ileum 28 days vs. MIRA control B6 ileum 8 month

value: B6. Knockout genes:Gpx1 or Gpx2. Phenotype:No intestinal inflammation. Gender:male. Age:28-days-old. Tissue:ileum

value: B6. Knockout genes:Gpx1 or Gpx2. Phenotype:No intestinal inflammation. Gender:mixed. Age:8-month-old. Tissue:ileum.


title: HAEC cells rep 2


title: 10_B6-129_ileum_8m_DKO-Tumor#91-vs-WT

source_name: Intestinal tumor from Gpx1/2-KO mouse#91


title: HAEC cells Intermittent Hypoxia rep 3


title: 9_B6-129_ileum_8m_DKO-vs-WT_2


title: 9_B6-129_ileum_8m_DKO-Tumor#86-vs-WT

source_name: Intestinal tumor from Gpx1/2-KO mouse#86


title: 4U_B6_ileum_8m_DKO-vs-WT_2

description: MIRA Gpx1/2-KO B6 ileum 8 month vs. MIRA control B6 ileum 8 month

value: B6. Knockout genes:Gpx1, Gpx2. Phenotype:Inflammatory Bowel diasease. Gender:mixed. Age:8-month-old. Tissue:ileum


title: 10_B6-129_ileum_8m_DKO-Tumor#3-vs-WT

source_name: Intestinal tumor from Gpx1/2-KO mouse#3


title: ARF-128

description: Comparative genomic hybridization


title: 9_B6-129_ileum_8m_DKO-Tumor#19-vs-WT

source_name: Intestinal tumor from Gpx1/2-KO mouse#19


title: 4L_B6_ileum_8m_DKO-vs-WT_3


title: 2_B6_liver_28d_DKO-vs-WT

description: MIRA Gpx1/2-KO B6 liver 28 days vs. MIRA control B6 liver 28 days

source_name: liver from Gpx1/2-KO mice

value: B6. Knockout genes:Gpx1, Gpx2. Phenotype:Inflammatory Bowel diasease. Gender:mixed. Age:28-days-old. Tissue:liver

source_name: liver from control mice

value: B6. Knockout genes:Gpx1 or Gpx2. Phenotype:No intestinal inflammation. Gender:mixed. Age:28-days-old. Tissue:liver.


title: 8_B6-129_ileum_8m_DKO-vs-WT_1


title: 5_B6_liver_8m_DKO-vs-WT_2

description: MIRA Gpx1/2-KO B6 liver 8 month vs. MIRA control B6 liver 8 month

value: B6. Knockout genes:Gpx1, Gpx2. Phenotype:Inflammatory Bowel diasease. Gender:mixed. Age:8-month-old. Tissue:liver

value: B6. Knockout genes:Gpx1 or Gpx2. Phenotype:No intestinal inflammation. Gender:mixed. Age:8-month-old. Tissue:liver.


title: 1U_B6_ileum_28d_DKO-vs-WT

description: MIRA Gpx1/2-KO B6 ileum 28 days vs. MIRA control B6 ileum 28 days

value: B6. Knockout genes:Gpx1, Gpx2. Phenotype:Inflammatory Bowel diasease. Gender:mixed. Age:28-days-old. Tissue:ileum

value: B6. Knockout genes:Gpx1 or Gpx2. Phenotype:No intestinal inflammation. Gender:mixed. Age:28-days-old. Tissue:ileum.


title: Time 30 min. without glucose   Replicate 1

status: Public on Dec 20 2008

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: Extraction using Agilent's Feature Extraction software

hyb_protocol: Agilent standard protocol 17H at 60 degrees C; Agilent proprietary Buffers

scan_protocol: Agilent scanner, 100% PMT

data_processing: Lowess on Background subtracted values using Genespring

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: Staphylococcus aureus Newman isogenic mutant ccpA-deficient

label_protocol: Direct labelling using RT and Cy5 dCTP

extract_protocol: RNeasy Kit from Qiagen

tag: isogenic mutant ccpA-deficient grown without Glucose, time=30 min.

source_name: Staphylococcus aureus Newman

label_protocol: Direct labelling using RT and Cy3 dCTP

tag: Staphylococcus aureus Newman


title: Time 30min. with glucose   Replicate 2

tag: isogenic mutant ccpA-deficient with Glucose, time=30 min.


title: 2_B6_liver_8m_DKO-vs-WT_1


title: Time 0   Replicate 2

tag: isogenic mutant ccpA-deficient


title: Time 30min. with glucose   Replicate 1


title: Time 0   Replicate 1


title: 10_B6-129_ileum_8m_DKO-Tumor#13-vs-WT

source_name: Intestinal tumor from Gpx1/2-KO mouse#13


title: Time 30 min. without glucose   Replicate 2

tag: isogenic mutant ccpA-deficient without Glucose, time=30 min.


title: S2 cell culture 4 replicate 1 at time 24h post Buchnera aphidicola APS infection

status: Public on Dec 15 2008

first: Roslin

last: Russell

address: Downing Street

department: Department of Genetics

hyb_protocol: Hybridisation to amino-modified long oligonucleotide microarrays using a Genomic Solutions hybridisation station with the Biosolutions hybridisation buffer (http://www.flychip.org.uk/protocols/hybridisation/hyb_oligoMWG.pdf)

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/scanning2.pdf

data_processing: Spot finding and quantitation via the Dapple package.

organism: Drosophila melanogaster

label_protocol: Reverse transcription and direct labelling for cDNA and oligo arrays (http://www.flychip.org.uk/protocols/gene_expression/direct_labelling.pdf) using 40ug of total RNA.

growth_protocol: Drosophila melanogaster S2 cells experimentally growing in Schneider's Drosophila medium supplemented with 10% foetal calf serum.

extract_protocol: Medium scale Trizol extraction (http://www.flychip.org.uk/protocols/gene_expression/standard_extraction.pdf).

source_name: pool

extract_protocol: Medium scale Trizol extraction (http://www.flychip.org.uk/protocols/gene_expression/medium_extraction.php).

tag: pool of S2 cells not exposed to Buchnera aphidicola APS


title: S2 cell culture 4 replicate 2 at time 24h post Buchnera aphidicola APS infection


title: S2 cell culture 3 replicate 1 at time 24h post Buchnera aphidicola APS infection


title: S2 cell culture 3 replicate 2 at time 24h post Buchnera aphidicola APS infection


title: S2 cell culture 2 replicate 1 at time 24h post Buchnera aphidicola APS infection


title: S2 cell culture 2 replicate 2 at time 24h post Buchnera aphidicola APS infection


title: 1L_B6_ileum_8m_DKO-vs-WT_1

source_name: intestinal epithelium from Gpx1/2-KO mice


title: S2 cell culture 1 replicate 2 at time 24h post Buchnera aphidicola APS infection


title: S2 cell culture 4 replicate 2 at time 1h post Buchnera aphidicola APS infection


title: S2 cell culture 1 replicate 1 at time 24h post Buchnera aphidicola APS infection


title: S2 cell culture 4 replicate 2 at time 6h post Buchnera aphidicola APS infection


title: S2 cell culture 3 replicate 2 at time 6h post Buchnera aphidicola APS infection


title: S2 cell culture 3 replicate 1 at time 1h post Buchnera aphidicola APS infection


title: S2 cell culture 1 replicate 2 at time 6h post Buchnera aphidicola APS infection


title: S2 cell culture 2 replicate 1 at time 1h post Buchnera aphidicola APS infection


title: S2 cell culture 2 replicate 2 at time 1h post Buchnera aphidicola APS infection


title: S2 cell culture 1 replicate 1 at time 6h post Buchnera  aphidicola APSinfection


title: S2 cell culture 3 replicate 1 at time 6h post Buchnera aphidicola APS infection


title: S2 cell culture 2 replicate 1 at time 6h post Buchnera aphidicola APS infection


title: S2 cell culture 4 replicate 1 at time 1h post Buchnera aphidicola APS infection